Two rails have it's advantage and disadvantage.
Good: You can connect the CPU to one and the video card and HDD's to the other. This divides the load more effectively.
Bad: If the amps on either rail are a little low a really high end CPU (AMD dual core and the FX series and the newer P4 3.2GHz) can overload either rail.
Why manufactures do it: It's actually cheaper to build 2X18A outputs then it is to build 1X36A output. For example a FET that can drive 20Amps might cost $5-10, but a FET that can handle 40Amps will cost $25.
IMO for a high end CPU and graphics card you're best to stick with a single high current 12Volt output supply. For a more moderate system, but with lots of HDD and DVD's etc, probably best to go with a dual 12V PSU.
Cheers.